Implementing theory_covmat action call in vp-setupfit + I/O of covmats
Created by: RosalynLP
As described in Issue #229 (closed)
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(Apr 30, 2025 7:42pm UTC)
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requested review from @enocera
requested review from @enocera
requested review from @enocera
Created by: RosalynLP
Maybe I misunderstood what to do but currently I get errors when I try to run this:
vp-setupfit NNPDF31_nlo_as_0118_new.yaml Traceback (most recent call last): File "/home/rosalyn/miniconda3/envs/nnpdf-dev/bin/vp-setupfit", line 11, in <module> load_entry_point('validphys', 'console_scripts', 'vp-setupfit')() File "/home/rosalyn/nnpdfgit/nnpdf/validphys2/src/validphys/scripts/vp_setupfit.py", line 143, in main a.main() File "/home/rosalyn/miniconda3/envs/nnpdf-dev/lib/python3.6/site-packages/reportengine/app.py", line 370, in main self.init() File "/home/rosalyn/nnpdfgit/nnpdf/validphys2/src/validphys/app.py", line 109, in init super().init() File "/home/rosalyn/miniconda3/envs/nnpdf-dev/lib/python3.6/site-packages/reportengine/app.py", line 282, in init args = self.get_commandline_arguments(cmdline) File "/home/rosalyn/nnpdfgit/nnpdf/validphys2/src/validphys/scripts/vp_setupfit.py", line 111, in get_commandline_arguments args = super().get_commandline_arguments(cmdline) File "/home/rosalyn/miniconda3/envs/nnpdf-dev/lib/python3.6/site-packages/reportengine/app.py", line 221, in get_commandline_arguments args = vars(self.argparser.parse_args(cmdline)) File "/home/rosalyn/nnpdfgit/nnpdf/validphys2/src/validphys/scripts/vp_setupfit.py", line 107, in argparser default=None) File "/home/rosalyn/miniconda3/envs/nnpdf-dev/lib/python3.6/argparse.py", line 1352, in add_argument return self._add_action(action) File "/home/rosalyn/miniconda3/envs/nnpdf-dev/lib/python3.6/argparse.py", line 1715, in _add_action self._optionals._add_action(action) File "/home/rosalyn/miniconda3/envs/nnpdf-dev/lib/python3.6/argparse.py", line 1556, in _add_action action = super(_ArgumentGroup, self)._add_action(action) File "/home/rosalyn/miniconda3/envs/nnpdf-dev/lib/python3.6/argparse.py", line 1366, in _add_action self._check_conflict(action) File "/home/rosalyn/miniconda3/envs/nnpdf-dev/lib/python3.6/argparse.py", line 1505, in _check_conflict conflict_handler(action, confl_optionals) File "/home/rosalyn/miniconda3/envs/nnpdf-dev/lib/python3.6/argparse.py", line 1514, in _handle_conflict_error raise ArgumentError(action, message % conflict_string) argparse.ArgumentError: argument -o/--output: conflicting option strings: -o, --outputAm I calling this in the wrong way or something? It has some problem with arguments so is this an issue with my config file? It is the same config file I used to test
vp-setupfitbefore, however.Created by: Zaharid
This doesn't work because
$ vp-setupfit testconfig.yml -o test (nnpdf-dev) [ERROR]: Bad configuration encountered: A parameter is required: theoryids. This is needed to process: - ('theory',) trough: - theory_covmat trough: - theoryids_experiments_central_values Maybe you mistyped theoryids in one of the following keys? - theoryCreated by: RosalynLP
When I try to update reportengine it has a problem:
`` Solving environment: failed
CondaHTTPError: HTTP 000 CONNECTION FAILED for url https://zigzah.com/static/conda-pkgs-private/noarch/repodata.json Elapsed: -
An HTTP error occurred when trying to retrieve this URL. HTTP errors are often intermittent, and a simple retry will get you on your way. SSLError(MaxRetryError('HTTPSConnectionPool(host='zigzah.com', port=443): Max retries exceeded with url: /static/conda-pkgs-private/noarch/repodata.json (Caused by SSLError(SSLError("bad handshake: Error([('SSL routines', 'ssl3_get_server_certificate', 'certificate verify faile
Created by: Zaharid
That is my private server. Should move the packages out of there. Fixed now.
On Wed, Aug 1, 2018 at 3:16 PM, RosalynLP notifications@github.com wrote:
Is this due to the server being broken still?
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Created by: RosalynLP
So I have added a section like this:
############################################################ # theory covmat default_theory: - theoryid: 163 theoryids: - 163 - 165 - 164 ############################################################to the config file (presumably it doesn't matter where?) in order to provide the relevant theories. I started with 3pt for simplicity. However, I got a bit confused about the syntax for
vp-setupfit- so far I havefile_content['actions_'] = ['datacuts check_t0pdfset', 'theory check_positivity', 'datacuts::closuretest::theory::fitting filter', 'theory theory_covmat']but in the code call you mentioned something like using a syntax
theory col col theory_config theory_covmat.
I don't understand what the theory_config is here; is it some tag I should have put in the config file somehow? Also I don't really understand the syntax of the columns.
Created by: voisey
When I run vp-setupfit on an example config file with
theory: theoryid: 163 # database id theoryids: - 163 - 165 - 164in the config file I get the following error:
[ERROR]: Bad configuration encountered: A parameter is required: experiment_result_table. This is needed to process: - theory_covmat trough: - theoryids_experiments_central_values trough: - experiments_central_values Maybe you mistyped experiment_result_table in one of the following keys? - experimentsHow do we specify experiment_result_table?
Also, @Zaharid, what is this 'theory col col theory_config theory_covmat' business that @RosalynLP mentioned above?
Created by: voisey
Thanks @Zaharid, I've fixed that now. I also had to specify a PDF set in the config file to process theory_covmat, so now there is a section in the test config file that reads:
theory: theoryid: 163 # database id theoryids: - 163 - 165 - 164 pdf: NNPDF31_nlo_as_0118With this vp-setupfit now downloads the relevant PDF set, filters the data, and verifies the positivity tables, but it then produces the following error:
[CRITICAL]: Bug in setup-fit ocurred. Please report it. Traceback (most recent call last): File "/var/pcfst/r02/theory/voisey/nnpdfgit/nnpdf/validphys2/src/validphys/scripts/vp_setupfit.py", line 126, in run super().run() File "/var/pcfst/r02/theory/voisey/nnpdfgit/nnpdf/validphys2/src/validphys/app.py", line 134, in run super().run() File "/usera/voisey/miniconda3/envs/vp2-env/lib/python3.6/site-packages/reportengine/app.py", line 359, in run rb.execute_sequential() File "/usera/voisey/miniconda3/envs/vp2-env/lib/python3.6/site-packages/reportengine/resourcebuilder.py", line 165, in execute_sequential *self.resolve_callargs(callspec)) File "/usera/voisey/miniconda3/envs/vp2-env/lib/python3.6/site-packages/reportengine/resourcebuilder.py", line 151, in resolve_callargs environment=self.environment,) File "/usera/voisey/miniconda3/envs/vp2-env/lib/python3.6/site-packages/reportengine/table.py", line 64, in prepare_path path = environment.table_folder / (name + '.csv') AttributeError: 'SetupFitEnvironment' object has no attribute 'table_folder'Do I need to specify the table_folder somehow?
Created by: Zaharid
The
SetupFitEnvironmentdoesn't forward the init_output method, which initializes these folders. Maybe having that environment thing wasn't a good idea. Anyway, I think this patch should work:--- a/validphys2/src/validphys/scripts/vp_setupfit.py +++ b/validphys2/src/validphys/scripts/vp_setupfit.py @@ -71,15 +71,10 @@ class SetupFitEnvironment(Environment): # check if results folder exists self.output_path = pathlib.Path(self.output_path).absolute() - if self.output_path.exists(): - log.warning(f"Output folder exists: {self.output_path} Overwritting contents") - else: - if not re.fullmatch(r'[\w.\-]+', self.output_path.name): - raise SetupFitError("Invalid output folder name. Must be alphanumeric.") - try: - self.output_path.mkdir() - except OSError as e: - raise EnvironmentError_(e) from e + if not re.fullmatch(r'[\w.\-]+', self.output_path.name): + raise SetupFitError("Invalid output folder name. Must be alphanumeric.") + + super().init_output()Created by: Zaharid
Please commit it.
On Thu, 16 Aug 2018, 17:10 Cameron Voisey, notifications@github.com wrote:
Yes, this makes things work, thanks. A tables folder is now produced with an experiment_result_table file for each of the three theoryids and a theory_covmat file. Shall I commit the patch now or will you?
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